Wgcna For Multiple Experiments

Question

[pixie@bioinfo]

I have performed WGCNA analysis on a single experiment corresponding to one GSE id in NCBI GEO. There are more such experiments for similar conditions corresponding to different GSE ids in GEO. I would like to include all those experiments and perform WGCNA analysis. How should I go about it ? (the experiments could be of different platforms).

Answer 1

[ewre]

it is not a good idea to integrate micro-array data of different platforms for 2 reasons:

1. data heterogeneity is a big problem for this kind of data.
2. usually different platforms have different probe designs and may cover different aspects of transcriptome,trying to get the intersect part will lose lots of probes

U can do WGCNA separately on these data and try to find if there are any coincidence among the high level results(such as pathway functional enrichment).